Analytical-grade formic acid (FA) was obtained from Honeywell Fluka (Roskilde, Denmark). LC-grade acetonitrile (ACN), LC-MS-grade water, ammonium formate, DL-LAN and L-Lysine-d4 were obtained from Sigma-Aldrich (St. Louis, MO, USA). DL-cystine-d4 was obtained from Cambridge Isotope Laboratories (Tewksbury, MA, USA). Analytical standards of LAL, CEL, CEL-d4, CML, CML-d4, furosine and furosine-d4 were from Iris Biotech GmbH (Marktredwitz, Germany). No commercial standard of histidinoalanine is available; therefore, it was not included.
Lc ms grade water
Manufactured by Merck Group
Sourced in Germany, United States, Italy, United Kingdom, India
LC-MS grade water is a highly purified water specifically designed for use in liquid chromatography-mass spectrometry (LC-MS) applications. It is produced to meet the stringent purity requirements necessary for sensitive analytical techniques.
Automatically generated - may contain errors
Lab products found in correlation
Acetonitrile, by Merck Group (37 mentions)
Methanol, by Merck Group (37 mentions)
Formic acid, by Merck Group (31 mentions)
Ammonium formate, by Merck Group (13 mentions)
Lc ms grade acetonitrile, by Merck Group (11 mentions)
Lc ms grade methanol, by Merck Group (10 mentions)
Gallic acid, by Merck Group (6 mentions)
Dithiothreitol (dtt), by Merck Group (6 mentions)
Acetic acid, by Merck Group (5 mentions)
Caffeic acid, by Merck Group (4 mentions)
Quercetin, by Merck Group (4 mentions)
Phosphate buffered saline (pbs), by Merck Group (4 mentions)
Ethanol, by Merck Group (4 mentions)
Trichloroacetic acid, by Merck Group (4 mentions)
Ammonium bicarbonate, by Merck Group (4 mentions)
Dimethyl sulfoxide (dmso), by Merck Group (4 mentions)
Sequencing grade modified trypsin, by Promega (4 mentions)
Ammonium acetate salt, by Merck Group (3 mentions)
Hydrogen peroxide, by Merck Group (3 mentions)
Lc ms grade, by Merck Group (3 mentions)
134 protocols using lc ms grade water
1
Analytical Standards for Glycation Products
2
Antioxidant Profiling of Algerian Black Cumin
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All chemicals and reagents used in this study were analytical grade. The chemicals such as 2,2′-diphenyl-1-picrylhydrazyl radical (DPPH•), absolute ethanol (99.9%, v/v) and sodium carbonate (Na2CO3) were purchased from Merck (Darmstadt, Germany). LC-MS grade water, ethanol and acetonitrile were obtained from Sigma–Aldrich (Steinheim, Germany), while trifluoroacetic acid (TFA) bought from Merck (Darmstadt, Germany). Catechin, myricetin, and quercitrin were provided by HWI ANALYTIK GMBH, while quercetin, epicatechin, sinapic acid, caffeic acid and gallic acid were acquired from Sigma–Aldrich (St. Louis, MO, USA). Rutin was purchased from PhytoLab GmbH & Co (Vestenbergsgreuth, Germany). Black cumin (Nigella sativa L.) seeds were obtained from a local market in Mascara City (Mascara, Algeria) in March 2022.
3
Protein A/agarose beads purification
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LC/MS CHROMASOLV® grade isopropanol (IPA), acetonitrile (ACN), LC-MS grade water, acetic acid (HAc), and phosphate buffered saline (PBS) were purchased from Sigma-Aldrich (St. Louis, MO). Pierce™ Trifluoroacetic acid (TFA), Bond-Breaker™ TCEP solution, Protein A/agarose beads, and papain were obtained from ThermoFisher Scientific (Hanover Park, IL). The packing materials for packing C5 (Jupiter particles, 5 µm diameter, 300 Å pore size) was purchased from Phenomenex (Torrance, CA). Amicon concentrators (10 kDa and 30 kDa) were obtained from Millipore (Burlington, MA).
4
Purification and Characterization of Protein Complexes
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Lyophilized HEWL, Cyt-c, RNase A, and HSA were purchased from Sigma-Aldrich and used without further purification or manipulation. Pt compounds, i.e., complex Pt2c, Pt-VIII, and Pt-IV, were synthesized as previously described [7 (link),8 (link)]. DMSO was purchased from Fluka. LC-MS grade water, methanol, and ammonium acetate salt were purchased from Sigma-Aldrich.
5
Enzymatic Removal of Emerging Pollutants
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All emerging pollutants were obtained from Sigma-Aldrich. Solvents used in LC-MS like LC-MS grade water, acetonitrile, and formic acid as well as Hydrogen peroxide was purchased from Sigma-Aldrich. Universal buffers were used in all experiments (0.2 M potassium phosphate (K2HPO4) and 0.1 M citrate acid). The specific enzymes activity for SBP, CPO, LPO MnP and HRP were 2700 IU/mg (1 mg/mL, 26 μM), 1296 IU/mg (17 mg/mL, 405 μM), (10 mg/mL, 26 μM), 200 IU/g (1 mg/mL, 26 μM) and 279 IU/mg (1 mg/mL, 26 μM) respectively. The enzymes (SBP, CPO, and LPO) were purchased from Bio-Research Products (North Liberty, USA). The enzymes (MnP and HRP) they were purchased from Sigma-Aldrich.
6
Anesthesia and Metabolite Quantification Protocol
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The drugs used for anesthesia were isoflurane
(Abbott, Maidenhead, U.K.) and urethane (Sigma, Gillingham, U.K.).
Ringer’s solution (sodium chloride, potassium chloride, calcium
chloride, and sodium bicarbonate) used as microdialysis perfusate
was obtained from Baxter (Northampton, U.K.). Solvents for metabolite
extraction from microdialysates (LC–MS grade water and methanol)
were obtained from Sigma (Gillingham, U.K.). Prepared samples were
placed in Total Recovery MS vials (Waters) for UPLC–MS analysis.
The chromatography solvents were water (LC–MS Chromasolv grade;
Sigma) and methanol (LC–MS Chromasolv grade; Sigma), used with
an HSS T3 column (1.8 μm, 100 mm × 2.1 mm; Waters Corporation,
U.S.A.). Formic acid, leucine enkephalin, and sodium formate were
obtained from Sigma. Nicotinamide (niacinamide) and uric acid, used
as standards, were also obtained from Sigma.
(Abbott, Maidenhead, U.K.) and urethane (Sigma, Gillingham, U.K.).
Ringer’s solution (sodium chloride, potassium chloride, calcium
chloride, and sodium bicarbonate) used as microdialysis perfusate
was obtained from Baxter (Northampton, U.K.). Solvents for metabolite
extraction from microdialysates (LC–MS grade water and methanol)
were obtained from Sigma (Gillingham, U.K.). Prepared samples were
placed in Total Recovery MS vials (Waters) for UPLC–MS analysis.
The chromatography solvents were water (LC–MS Chromasolv grade;
Sigma) and methanol (LC–MS Chromasolv grade; Sigma), used with
an HSS T3 column (1.8 μm, 100 mm × 2.1 mm; Waters Corporation,
U.S.A.). Formic acid, leucine enkephalin, and sodium formate were
obtained from Sigma. Nicotinamide (niacinamide) and uric acid, used
as standards, were also obtained from Sigma.
7
SILAC Proteomic Workflow for LC-MS/MS
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SILAC labeling was performed by growing cells for at least five passages in lysine- and arginine-free SILAC medium (RPMI, Invitrogen) supplemented with 10% dialyzed fetal calf serum, 2 mM L-glutamine and 1% P/S. “Light” and “heavy” media were supplemented with natural lysine and arginine (0.1 mg/mL), and 13C-, 15N-labeled lysine and arginine (0.1 mg/mL), respectively.
General protein digestion for LC-MS/MS analysis was performed by dissolving protein (e.g. whole lysate or enriched proteins) in digestion buffer (8 M urea, 50 mM NH4HCO3, pH 8.0), followed by disulfide reduction with DTT (10 mM, 40 minutes, 50 ˚C), alkylation (iodoacetamide, 15 mM, 30 min, room temperature, protected from light) and quenching (DTT, 5mM, 10 minutes, room temperature). The proteome solution was diluted 4-fold with ammonium bicarbonate solution (50 mM, pH 8.0), CaCl2 added (1 mM) and digested with sequencing grade trypsin (∼1:100 enzyme/protein ratio; Promega) at 37 ˚C while rotating overnight. Peptide digestion reactions were stopped by acidification to pH 2-3 with 1% formic acid, and peptides were then desalted on ZipTip C18 tips (100 μL, Millipore), dried under vacuum, resuspended with LC-MS grade water (Sigma Aldrich), and then lyophilized. Lyophilized peptides were dissolved in LC-MS/MS Buffer A (H2O with 0.1% formic acid, LC-MS grade, Sigma Aldrich) for proteomic analysis.
General protein digestion for LC-MS/MS analysis was performed by dissolving protein (e.g. whole lysate or enriched proteins) in digestion buffer (8 M urea, 50 mM NH4HCO3, pH 8.0), followed by disulfide reduction with DTT (10 mM, 40 minutes, 50 ˚C), alkylation (iodoacetamide, 15 mM, 30 min, room temperature, protected from light) and quenching (DTT, 5mM, 10 minutes, room temperature). The proteome solution was diluted 4-fold with ammonium bicarbonate solution (50 mM, pH 8.0), CaCl2 added (1 mM) and digested with sequencing grade trypsin (∼1:100 enzyme/protein ratio; Promega) at 37 ˚C while rotating overnight. Peptide digestion reactions were stopped by acidification to pH 2-3 with 1% formic acid, and peptides were then desalted on ZipTip C18 tips (100 μL, Millipore), dried under vacuum, resuspended with LC-MS grade water (Sigma Aldrich), and then lyophilized. Lyophilized peptides were dissolved in LC-MS/MS Buffer A (H2O with 0.1% formic acid, LC-MS grade, Sigma Aldrich) for proteomic analysis.
8
Lipidomics Analysis of Sphingolipids
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Propan-2-one, methanol, 1-butanol, LC-MS grade water, primuline yellow dye, ammonium dihydrogen phosphate, 3,5-Di-tert-4-butylhydroxytoluene (BHT) and ammonium formate were from Sigma-Aldrich (Saint Louis, MO, USA). Ethanol and high performance liquid chromatography (HPLC)-analytical grade chloroform (CHCl3) were respectively from J.T. Baker (Center Valley, PA, USA) and Carlo Erba (Cornaredo, MI, Italy). N-lignoceroyl-D-erythro-sphingosine (Cer C24:0) 1,2-Dipalmitoyl-sn-Glycero-3-Phosphocholine (DPPC), Cardiolipin (CL), 1,2-Dipalmitoyl-sn-Glycero-3-Phosphoethanolamine (DPPE), D-glucosyl-ß-1,1′-N-stearoyl-D-erythro-sphingosine-d5 (HexCer), N-lauroyl-D-erythro-sphingosine, N-lauroyl-D-erythro-sphinganine, N-lauroyl-D-erythro-sphingosylphosphorylcholine N-lauroyl-D-erythro-sphinganylphosphorylcholine, D-glucosyl-ß−1,1′-N-lauroyl-D-erythro-sphingosine, D-lactosyl-ß-1,1′ N-lauroyl-D-erythro-sphingosine and C17 d-erythro-dihydrosphingosine-1-phosphate lipids standards were from Avanti Polar Lipids (Alabaster, Alabama, USA). SL standard mixture, containing SM and Sulfatides (SLF) was from Matreya LLC (Pleasant Gap, PA, USA).
9
Quantitative Analysis of Oxidative Stress Biomarkers
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Resveratrol, L-(+)-tartaric acid, quercetin, (+)-catechin hydrate sulfatase (Helix pomatia, Type H-1, sulfatase ≥ 10,000 units/g), and β-glucuronidase (Helix pomatia, Type HP-2, ≥100,000 units/mL) were purchased from Sigma-Aldrich (St. Louis, MO, USA). 8-iso prostaglandin F2α and 8-iso prostaglandin F2α-d4 were purchased from Cayman Chemical Company (Ann Arbor, MI, USA). (±)-Tartaric-2,3-d2 acid was purchased from C/D/N Isotopes (QC, Pointe-Claire, QC, Canada). Fisetin and formic acid (LC-MS grade) were obtained from TCI chemicals (Portland, OR, USA). LC-MS grade water and acetonitrile were purchased from Sigma-Aldrich (St. Louis, MO, USA). A creatinine parameter assay kit was purchased from R&D systems (Minneapolis, MN, USA), and Millex-GV Filter (0.22 µm) was obtained from EMD Millipore (Burlington, MA, USA).
10
SILAC Proteomic Workflow for LC-MS/MS
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